CFSA: Comparative flux sampling analysis as a guide for strain design
Genome-scale metabolic models of microbial metabolism have extensively been used to guide the design of microbial cell factories, still, many of the available strain design algorithms often fail to produce a reduced list of targets for improved performance that can be implemented and validated in a...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-12-01
|
| Series: | Metabolic Engineering Communications |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214030124000130 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846119460773036032 |
|---|---|
| author | R.P. van Rosmalen S. Moreno-Paz Z.E. Duman-Özdamar M. Suarez-Diez |
| author_facet | R.P. van Rosmalen S. Moreno-Paz Z.E. Duman-Özdamar M. Suarez-Diez |
| author_sort | R.P. van Rosmalen |
| collection | DOAJ |
| description | Genome-scale metabolic models of microbial metabolism have extensively been used to guide the design of microbial cell factories, still, many of the available strain design algorithms often fail to produce a reduced list of targets for improved performance that can be implemented and validated in a step-wise manner. We present Comparative Flux Sampling Analysis (CFSA), a strain design method based on the extensive comparison of complete metabolic spaces corresponding to maximal or near-maximal growth and production phenotypes. The comparison is complemented by statistical analysis to identify reactions with altered flux that are suggested as targets for genetic interventions including up-regulations, down-regulations and gene deletions. We applied CFSA to the production of lipids by Cutaneotrichosporon oleaginosus and naringenin by Saccharomyces cerevisiae identifying engineering targets in agreement with previous studies as well as new interventions. CFSA is an easy-to-use, robust method that suggests potential metabolic engineering targets for growth-uncoupled production that can be applied to the design of microbial cell factories. |
| format | Article |
| id | doaj-art-27751fbd27aa4962a865fd9ac60294b5 |
| institution | Kabale University |
| issn | 2214-0301 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Metabolic Engineering Communications |
| spelling | doaj-art-27751fbd27aa4962a865fd9ac60294b52024-12-17T04:59:36ZengElsevierMetabolic Engineering Communications2214-03012024-12-0119e00244CFSA: Comparative flux sampling analysis as a guide for strain designR.P. van Rosmalen0S. Moreno-Paz1Z.E. Duman-Özdamar2M. Suarez-Diez3Laboratory of Systems and Synthetic Biology, Stippeneng 4 6708 WE Wageningen, the NetherlandsLaboratory of Systems and Synthetic Biology, Stippeneng 4 6708 WE Wageningen, the NetherlandsLaboratory of Systems and Synthetic Biology, Stippeneng 4 6708 WE Wageningen, the NetherlandsCorresponding author.; Laboratory of Systems and Synthetic Biology, Stippeneng 4 6708 WE Wageningen, the NetherlandsGenome-scale metabolic models of microbial metabolism have extensively been used to guide the design of microbial cell factories, still, many of the available strain design algorithms often fail to produce a reduced list of targets for improved performance that can be implemented and validated in a step-wise manner. We present Comparative Flux Sampling Analysis (CFSA), a strain design method based on the extensive comparison of complete metabolic spaces corresponding to maximal or near-maximal growth and production phenotypes. The comparison is complemented by statistical analysis to identify reactions with altered flux that are suggested as targets for genetic interventions including up-regulations, down-regulations and gene deletions. We applied CFSA to the production of lipids by Cutaneotrichosporon oleaginosus and naringenin by Saccharomyces cerevisiae identifying engineering targets in agreement with previous studies as well as new interventions. CFSA is an easy-to-use, robust method that suggests potential metabolic engineering targets for growth-uncoupled production that can be applied to the design of microbial cell factories.http://www.sciencedirect.com/science/article/pii/S2214030124000130Metabolic engineeringGenome scale metabolic modellingFlux sampling |
| spellingShingle | R.P. van Rosmalen S. Moreno-Paz Z.E. Duman-Özdamar M. Suarez-Diez CFSA: Comparative flux sampling analysis as a guide for strain design Metabolic Engineering Communications Metabolic engineering Genome scale metabolic modelling Flux sampling |
| title | CFSA: Comparative flux sampling analysis as a guide for strain design |
| title_full | CFSA: Comparative flux sampling analysis as a guide for strain design |
| title_fullStr | CFSA: Comparative flux sampling analysis as a guide for strain design |
| title_full_unstemmed | CFSA: Comparative flux sampling analysis as a guide for strain design |
| title_short | CFSA: Comparative flux sampling analysis as a guide for strain design |
| title_sort | cfsa comparative flux sampling analysis as a guide for strain design |
| topic | Metabolic engineering Genome scale metabolic modelling Flux sampling |
| url | http://www.sciencedirect.com/science/article/pii/S2214030124000130 |
| work_keys_str_mv | AT rpvanrosmalen cfsacomparativefluxsamplinganalysisasaguideforstraindesign AT smorenopaz cfsacomparativefluxsamplinganalysisasaguideforstraindesign AT zedumanozdamar cfsacomparativefluxsamplinganalysisasaguideforstraindesign AT msuarezdiez cfsacomparativefluxsamplinganalysisasaguideforstraindesign |